Genomatix ChipInspector is an automated bioinformatics software package specifically designed for high-quality microarray analysis (such as Affymetrix, Illumina, Agilent, and NimbleGen). Unlike traditional analysis tools that rely on pre-defined “probe sets” (which average out values and lose transcript-specific data), ChipInspector utilizes a single-probe analysis approach. This allows you to bypass complex interpolation errors, lower false-positive rates, and map changes directly to alternative transcripts and precise genomic locations.
Note: The traditional Genomatix suite has shifted towards modern integrated pipelines like the Genomatix Genome Analyzer. However, the core algorithmic workflow of ChipInspector remains a foundational blueprint for raw single-probe microarray mining. Step 1: Raw Data Import
Format Compatibility: Locate and upload your raw microarray data files. ChipInspector natively accepts raw cell intensity files, most notably Affymetrix .CEL files, as well as formats from Agilent and Illumina.
Avoid Summarization: Ensure you are importing raw single-probe intensity values rather than data pre-summarized by manufacturer software (like Affymetrix Expression Console). Step 2: Single-Probe Normalization An Integrated Workflow for Analysis of ChIP-Chip Data